Unique Mitochondrial Single Nucleotide Polymorphisms Demonstrate Resolution Potential to Discriminate Theileria Parva Vaccine and Buffalo-Derived Strains

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Unique Mitochondrial Single Nucleotide Polymorphisms Demonstrate Resolution Potential to Discriminate Theileria Parva Vaccine and Buffalo-Derived Strains life Article Unique Mitochondrial Single Nucleotide Polymorphisms Demonstrate Resolution Potential to Discriminate Theileria parva Vaccine and Buffalo-Derived Strains Micky M. Mwamuye 1,* , Isaiah Obara 1, Khawla Elati 1, David Odongo 2 , Mohammed A. Bakheit 3, Frans Jongejan 4 and Ard M. Nijhof 1,* 1 Institute for Parasitology and Tropical Veterinary Medicine, Freie Universität Berlin, Robert-von-Ostertag-Str. 7-13, 14163 Berlin, Germany; [email protected] (I.O.); [email protected] (K.E.) 2 School of Biological Sciences, University of Nairobi, P.O. Box 30197-00100 Nairobi, Kenya; [email protected] 3 Department of Parasitology, Faculty of Veterinary Medicine, University of Khartoum, P.O. Box 321-11115 Khartoum, Sudan; [email protected] 4 Vectors and Vector-Borne Diseases Research Programme, Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Private Bag X04, 0110 Onderstepoort, South Africa; [email protected] * Correspondence: [email protected] (M.M.M.); [email protected] (A.M.N.); Tel.: +49-30-838-62326 (A.M.N.) Received: 16 November 2020; Accepted: 8 December 2020; Published: 8 December 2020 Abstract: Distinct pathogenic and epidemiological features underlie different Theileria parva strains resulting in different clinical manifestations of East Coast Fever and Corridor Disease in susceptible cattle. Unclear delineation of these strains limits the control of these diseases in endemic areas. Hence, an accurate characterization of strains can improve the treatment and prevention approaches as well as investigate their origin. Here, we describe a set of single nucleotide polymorphisms (SNPs) based on 13 near-complete mitogenomes of T. parva strains originating from East and Southern Africa, including the live vaccine stock strains. We identified 11 SNPs that are non-preferentially distributed within the coding and non-coding regions, all of which are synonymous except for two within the cytochrome b gene of buffalo-derived strains. Our analysis ascertains haplotype-specific mutations that segregate the different vaccine and the buffalo-derived strains except T. parva-Muguga and Serengeti-transformed strains suggesting a shared lineage between the latter two vaccine strains. Phylogenetic analyses including the mitogenomes of other Theileria species: T. annulata, T. taurotragi, and T. lestoquardi, with the latter two sequenced in this study for the first time, were congruent with nuclear-encoded genes. Importantly, we describe seven T. parva haplotypes characterized by synonymous SNPs and parsimony-informative characters with the other three transforming species mitogenomes. We anticipate that tracking T. parva mitochondrial haplotypes from this study will provide insight into the parasite’s epidemiological dynamics and underpin current control efforts. Keywords: Theileria parva; mitogenomes; haplotypes; SNPs; live vaccine 1. Introduction The protozoan parasite Theileria parva that causes East Coast fever (ECF) and Corridor Disease (CD) is considered among the most debilitating tick-borne pathogens in cattle over its endemic range Life 2020, 10, 334; doi:10.3390/life10120334 www.mdpi.com/journal/life Life 2020, 10, 334 2 of 16 in East, Central, and Southern Africa [1]. In typical ECF symptoms, the disease severity is mainly due to the parasites’ ability to transform host lymphocytes [2]. Parasitized lymphocytes proliferate uncontrollably and disseminate the dividing parasite into multiple host tissues. Their accumulation in the lungs triggers severe vasculitis, eventually resulting in respiratory failure with death occurring within three to four weeks of infection [3,4]. With mortalities of up to 100% in susceptible animals, an estimated one million die per year from an estimated risk population of 28 million cattle mainly belonging to livestock farmers with economically constrained livelihoods [5]. Thus, control of the parasite is urgent to livelihood improvement efforts among resource-poor farmers in sub-Saharan Africa, as highlighted by the World Organization for Animal Health (OIE) [6]. Current control methods include strict tick control measures to curtail pathogen transmission. However, this approach relies heavily on acaricide use, which is unsustainable in the long-run due to acaricide resistance challenges, and toxicity concerns in food and the environment [7]. Anti-theilerial chemotherapy is effective but only with early detection of the disease, which is impractical under field conditions [8,9]. Early observations that cattle acquire long-term immunity when challenged with infected ticks under a long-acting antibiotic treatment opened avenues for the development of an alternative control method based on live parasite stocks, which is called the infection and treatment method (ITM) [10,11]. ITM consists of inoculating cattle with cryopreserved T. parva sporozoites combined with simultaneous treatment with long-acting oxytetracyclines [12]. Early experiments revealed that there were varying cross-reactivities between geographical strains [13,14]. Due to this limitation, a cocktail of three immunizing parasite stocks known as the ‘Muguga cocktail’, comprising Serengeti-transformed, Kiambu 5, and Muguga strains, were combined to achieve broad protection against diverse field isolates [11]. Several other strains have been immunologically profiled to identify an isolate that cross-reacts to diverse field strains in ECF endemic areas. Among the identified strains was a Marikebuni stock isolated from the Kenyan Coast that showed cross-protection against several eastern African strains and, a Boleni strain from Zimbabwe which, apart from a cross-reactivity against Eastern and Central African strains, induced mild infections, hence eliminating the need for antibiotic use in ITM protocol [12]. Historically, ECF is traced to have originated from East Africa and spread southwards, first being reported in present-day Zimbabwe and eventually into South Africa [1]. Yet, it is notable that T. parva strains from different geographic regions have varying immunological profiles and epidemiological features. For example, an ability to induce a carrier state in which recovered animals remain infective to ticks has been demonstrated in some strains, enabling transmission between cattle by the vector tick, Rhipicephalus appendiculatus [15–17]. This persistence of vaccine strains raised initial concerns about spreading foreign parasite genotypes into endemic countries free of the vaccine parasite stocks, thereby possibly disrupting endemic stability [18]. By contrast, it is also known that some parasite strains, particularly of African buffalo (Syncerus caffer) origin, induce limited parasitosis and parasitemia, are non-persistent and not efficiently transmissible between cattle hosts [19]. These strains are known to cause a more acute clinical syndrome called Corridor Disease in areas where susceptible cattle are exposed to vector ticks infected on buffalo, which are the primary mammalian carrier hosts [20,21]. Based on its unique clinical presentation, which differs from classical ECF, these particular strains were initially recognized as Theileria parva lawrencei in earlier literature; however, this nomenclature was subsequently abolished with increasing molecular and antigenic data confirming similarities between the two strain populations [22–24]. Further, these data have revealed that cattle transmissible strains are a separately maintained subset population of those found in buffalo, and to differentiate between the two populations, T. parva strains are arbitrarily considered to be either of buffalo or cattle-derived for epidemiological reasons [25]. However, the genetic underpinnings of these strain differences are yet to be fully unraveled, and a precise delineation of the various genotypes is lacking [23]. This is partly because of the parasite’s biology, which renders it technically unamenable for genomic studies, especially in obtaining Life 2020, 10, 334 3 of 16 pure parasite DNA free from host-DNA contamination [26]. An accurate determination of the origin (buffalo or cattle derived) and geographic spread of strains will help intervention and control efforts. Additionally, accurate characterization of T. parva strains will help to track their frequency and distribution in specific populations, and to characterize breakthroughs in areas of live vaccine field deployments. Further, since T. parva has sexual reproductive phases that are associated with genetic recombination [27], unraveling the parasite genotypes could enhance the understanding of the long-term effects of live vaccine components in the field. Owing to limited or no recombination, uniparental inheritance patterns and a high substitution rate relative to nuclear genomes, mitochondrial genome studies on related apicomplexan parasites have provided clues of the geographical origin and variants of parasites [28,29]. However, the utility of mitochondrial genomes in T. parva in delimiting the strains and their geographical origin remains unexplored. In this study, we sequenced the mitochondrial genomes of ten T. parva strains, found within the parasite’s currently known endemic range, as well as some characterized isolates used as vaccine strains. We also included the mitogenomes of nine other T. parva isolates assembled from their whole-genome data that are publicly available [30]. Further, this study assessed the divergence of T. parva from the closely related host-leukocyte transforming species T. annulata,
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